HHsearch alignment for GI: 254780710 and conserved domain: TIGR00652

>TIGR00652 DapF diaminopimelate epimerase; InterPro: IPR001653 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see . The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria . The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants . This entry represents diaminopimelate epimerase (5.1.1.7 from EC), which catalyses the isomerisation of L,L-dimaminopimelate to meso-DAP in the biosynthetic pathway leading from aspartate to lysine. It is a member of the broader family of PLP-independent amino acid racemases. This enzyme is a monomeric protein of about 30 kDa consisting of two domains which are homologus in structure though they share little sequence similarity . Each domain consists of mixed beta-sheets which fold into a barrel around the central helix. The active site cleft is formed from both domains and contains two conserved cysteines thought to function as the acid and base in the catalytic reaction . Other PLP-independent racemases such as glutamate racemase have been shown to share a similar structure and mechanism of catalysis.; GO: 0008837 diaminopimelate epimerase activity, 0009089 lysine biosynthetic process via diaminopimelate.
Probab=100.00  E-value=0  Score=638.46  Aligned_cols=271  Identities=34%  Similarity=0.620  Sum_probs=240.9

Q ss_pred             CEEEEECCCCCCEEEEECCC--CCCCCC---HHHHHHHCC-CCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCC
Q ss_conf             11378517677389994778--887888---889987203-567143558998258888866899997178762123320
Q gi|254780710|r    6 VDFAKMEGIGNKILVIDMRG--CHDNIT---SDAINALST-DDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGN   79 (296)
Q Consensus         6 i~F~Kmhg~GNDFiiiD~~~--~~~~~~---~~~i~~~~~-~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGN   79 (296)
T Consensus         1 ~~F~KmhGlGNDFv~v~~~~eL~~~~~~~~kp~~~~~vc~r~~G~GaDG~i~v~~P~s~~~D~~~~iFNsDGS~A~mCGN   80 (294)
T TIGR00652         1 MEFSKMHGLGNDFVLVDEFDELAELVKEEEKPEFVRQVCDRHFGVGADGVIFVEPPGSPEADYKMRIFNSDGSEAEMCGN   80 (294)
T ss_pred             CEEEEEECCCCCEEEECCCHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCC
T ss_conf             92784321346579948904764421654338999999860481332527998569998863699999678980024766


Q ss_pred             HHHHHHHHHHCCC--CCCEEEEEECCCCEEEEECCCC----EEEECCCCCCCCHHHCCCCCCCCCCCCCE-EECCCCCCC
Q ss_conf             3322311100135--7640379835883799985774----27740368777777685656565434430-110577774
Q gi|254780710|r   80 GMRCVVRFLTSRM--KRKSFTFETIRGILVAKENRDG----SISVDMGEPILDWKLIPLARSFDKMDRDR-FHIGPVNHL  152 (296)
Q Consensus        80 G~Rc~a~yl~~~~--~~~~~~i~T~~g~~~~~~~~~~----~v~V~mG~p~~~~~~ip~~~~~~~~~~~~-~~~~~~~~~  152 (296)
T Consensus        81 G~RC~~~f~~~~~~~~k~~~~v~T~~G~~~~~~~~~ng~v~~v~VdMG~p~~~~~~~p~~~~~~~~~~~~~~~~~~~---  157 (294)
T TIGR00652        81 GIRCFAKFVYEHGLVEKKDIRVETLAGVIKLEVEEENGAVAKVKVDMGEPKFKKEEIPLTDKVEKFEEPEVLLFGEV---  157 (294)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCEEEEEEEECCCEEEEEEEECCCCCCCHHCCCHHCCCCCCCCCCEEEEECC---
T ss_conf             78999999986223421106998617348999997288599999853775344100510015454554522431033---


Q ss_pred             EECCEEEEECCCCEEEEECCCC--CCHHHHHHHHHCCCCCCCC-CCCCCEEEEEECCCCEEEEEECCCC-CCCCCCCHHH
Q ss_conf             0213099955874279742557--6868887631000233237-5555146799728872899980467-8766563235
Q gi|254780710|r  153 FLRNPFVVSMGNPHAIFFVEDD--LYHYDLASFGNLLAKHPMF-SEGVNLSIARVTSLESLDLRTWERG-VGLTAACGSA  228 (296)
Q Consensus       153 ~~~~~~~v~iGNPH~Vi~v~d~--i~~~~l~~~g~~i~~~~~F-p~gvNV~fv~v~~~~~I~iRt~ERG-vGeTlACGTG  228 (296)
T Consensus       158 ~~~~~~~v~~GnPH~v~fv~-d~~~~~~~~~~lG~~~~~he~F~Peg~NV~Fv~~~~~~~i~~rtyERGV~G~T~ACGTG  236 (294)
T TIGR00652       158 QTLKLTAVDTGNPHLVVFVD-DLTVEGLDLTELGPLLEYHERFAPEGVNVNFVQVVGEDEIKLRTYERGVAGETLACGTG  236 (294)
T ss_pred             CEEEEEEEECCCCEEEEECC-CCCCCCCCHHHHHHHHHCCCCCCCCCEEEEEEEECCCCEEEEEEEEECCCCCCCCCCHH
T ss_conf             33799999659966999805-55646467567747765383557687238898976898899999880544554465147


Q ss_pred             HHHHHHHHHH--HCCCCCC-EEEECCCCEEEEEEECCC--EEEEEECEEEEEEEEEE
Q ss_conf             8999999998--1788980-799907957999995898--19999462899988998
Q gi|254780710|r  229 ACASVVASGC--LHKTNRA-VSVKMLGGGLLIEWHDNN--HVFMTGEAKKEWEGKLD  280 (296)
Q Consensus       229 A~Asa~~~~~--~~~~~~~-v~V~~pGG~L~v~~~~~~--~i~l~Gpa~~vf~G~~~  280 (296)
T Consensus       237 a~A~a~aa~~~~~~~~~~~~~~V~~~gG~L~i~~~~~G~~~~ym~G~a~~V~~G~l~  293 (294)
T TIGR00652       237 ACASAIAAVKIGLGLTDKKAVTVHLPGGELEIEWKEDGKHRVYMTGPAVRVFDGELF  293 (294)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEECCCEEEEEEECCCCCEEEEEECEEEEEEEEEC
T ss_conf             999999998752045688616898169829999972885114687044688855653